Elantra XD (2001-06) :: Misfire - Consistently Getting Codes P0301 And P0304

I would like to find out why my car is misfiring before throwing parts at it. I have a basic level of mechanics and have checked a few things before posting here, which may or may not have ruled out some possibilities.

The problem: I have been consistently getting P0301 and P0304 but only happens sometimes, while other times there is no check engine light. I first checked the ignition coil, right side of it, that controls cylinders 1 and 4. Did resistance test, measured for voltage, and checked the wires for continuity to the connector, with everything coming out good. I know a few must have had issues with the cheap pigtail connector like me so I went and changed that but still got the misfire codes. I then put in an older known to be good working coil but no change.

After that, I removed spark plugs 1 and 4 and put them where 2 and 3 go but still got the same codes P0301 and P0304.

A friend who is a mechanic for Nissan checked the spark and wires, saying they were fine. He then checked the injectors and noticed that injector 1 didn't increase in ticking sound when RPM increased. He said I should replace injectors 1 and 4 to see if that changes anything or switch injectors 1 and 4 with 2 and 3 to see if the codes at least change. I removed them all, got two of them from junkyard just in case, made my own tool where I pumped straight fuel injector cleaner through each of them with pumped air, and put the two from junkyard on cylinders 1 and 4. I still got the same codes so then I switched injectors 1 and 4 with 2 and 3, which didn't change the codes.

I was told by another local mechanic shop that it's definitely the coil but I knew it wasn't.

Other info: I am not sure it would matter when dealing with a misfire but I borrowed a code scanner and saw that the Long Term Fuel Trim was -7%. I researched that and it means that the car is running rich and the computer is being told that it needs to run lean. I am not sure that this would make only two of the cylinders misfire and the freeze data shows that same negative LTFT for when the P0301 happened. I also know that there is an air leak at the gasket where the front cat connects to the flex pipe/rear cat. I have also gotten a rear downstream 02 sensor code once within the past month but it hasn't come back.

Would the LTFT being lean have anything to do with the misfires? Would the gasket between the two cats cause the 02 sensor to get a faulty reading? If so, would the downstream 02 sensor be able to adjust to a lean fuel mix? What else should I check?